bucher1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000328) Biomodels notes: Time courses as in figure 2 of the publication. Integration was performed using Copasi 4.6.33. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.
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| Simulation | |
|---|---|
| bucher2011_Fig2 |
Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.
| Name | Definition | |
|---|---|---|
| — | 60.0 second | |
| — | 1e-12 mole | |
| — | 0.001 litre | |
| — | 1e-09 mole litre^(-1.0) | |
| — | 1.6666666666666667e-14 mole second^(-1.0) | |
| — | 1.6666666666666667e-05 litre second^(-1.0) | |
| — | 1.0 dimensionless |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| cell | — | 3.0 | 0.0142 | |
| compartment | — | 3.0 | 1.0 | |
| medium | — | 3.0 | 2.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| ASL_b | — | 0.0 | cell | ✘ | |
| ASL_c | — | 0.0 | cell | ✘ | |
| ASL_m | — | 30.56 | medium | ✘ | |
| ASLoOH_b | — | 0.0 | cell | ✘ | |
| ASLoOH_c | — | 0.0 | cell | ✘ | |
| ASLoOH_m | — | 0.0 | medium | ✘ | |
| ASLpOH_b | — | 0.0 | cell | ✘ | |
| ASLpOH_c | — | 0.0 | cell | ✘ | |
| ASLpOH_m | — | 0.0 | medium | ✘ | |
| AS_b | — | 0.0 | cell | ✘ | |
| AS_c | — | 0.0 | cell | ✘ | |
| AS_m | — | 8797.15 | medium | ✘ | |
| ASoOH_b | — | 0.0 | cell | ✘ | |
| ASoOH_c | — | 0.0 | cell | ✘ | |
| ASoOH_m | — | 0.0 | medium | ✘ | |
| ASpOH_b | — | 0.0 | cell | ✘ | |
| ASpOH_c | — | 0.0 | cell | ✘ | |
| ASpOH_m | — | 0.0 | medium | ✘ |
Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.
| Definition |
|---|
| Id | Name | Objective coefficient | Reaction Equation and Kinetic Law | Flux bounds | |
|---|---|---|---|---|---|
| ASL_Prot | — | ASL_c > ASL_b Prot_k1 * ((1 - fu_ASL) / fu_ASL * ASL_c - ASL_b) | |||
| ASLoOH_Prot | — | ASLoOH_c > ASLoOH_b Prot_k1 * ((1 - fu_ASL) / fu_ASL * ASLoOH_c - ASLoOH_b) | |||
| ASLpOH_Prot | — | ASLpOH_c > ASLpOH_b Prot_k1 * ((1 - fu_ASL) / fu_ASL * ASLpOH_c - ASLpOH_b) | |||
| AS_Prot | — | AS_c > AS_b Prot_k1 * ((1 - fu_AS) / fu_AS * AS_c - AS_b) | |||
| ASoOH_Prot | — | ASoOH_c > ASoOH_b Prot_k1 * ((1 - fu_AS) / fu_AS * ASoOH_c - ASoOH_b) | |||
| ASpOH_Prot | — | ASpOH_c > ASpOH_b Prot_k1 * ((1 - fu_AS) / fu_AS * ASpOH_c - ASpOH_b) | |||
| CR_oOH | — | ASLoOH_c > ASoOH_c (k_CR_ASL_c + k_PON_OH_c) * ASLoOH_c | |||
| CR_pOH | — | ASLpOH_c > ASpOH_c (k_CR_ASL_c + k_PON_OH_c) * ASLpOH_c | |||
| CYP3A4_ASLoOH | — | ASL_c > ASLoOH_c CYP3A4_ASLoOH_Vmax / CYP3A4_ASLoOH_Km1 * ASL_c / (1 + AS_c / CYP3A4_ASpOH_Km1 + AS_c / CYP3A4_ASoOH_Km1 + ASL_c / CYP3A4_ASLpOH_Km1 + ASL_c / CYP3A4_ASLoOH_Km1) | |||
| CYP3A4_ASLpOH | — | ASL_c > ASLpOH_c CYP3A4_ASLpOH_Vmax / CYP3A4_ASLpOH_Km1 * ASL_c / (1 + AS_c / CYP3A4_ASpOH_Km1 + AS_c / CYP3A4_ASoOH_Km1 + ASL_c / CYP3A4_ASLpOH_Km1 + ASL_c / CYP3A4_ASLoOH_Km1) | |||
| CYP3A4_ASoOH | — | AS_c > ASoOH_c CYP3A4_ASoOH_Vmax / CYP3A4_ASoOH_Km1 * AS_c / (1 + AS_c / CYP3A4_ASpOH_Km1 + AS_c / CYP3A4_ASoOH_Km1 + ASL_c / CYP3A4_ASLpOH_Km1 + ASL_c / CYP3A4_ASLoOH_Km1) | |||
| CYP3A4_ASpOH | — | AS_c > ASpOH_c CYP3A4_ASpOH_Vmax / CYP3A4_ASpOH_Km1 * AS_c / (1 + AS_c / CYP3A4_ASpOH_Km1 + AS_c / CYP3A4_ASoOH_Km1 + ASL_c / CYP3A4_ASLpOH_Km1 + ASL_c / CYP3A4_ASLoOH_Km1) | |||
| Export_AS | — | AS_c > AS_m Export_AS_k * AS_c | |||
| Export_ASL | — | ASL_c > ASL_m Export_ASL_k * ASL_c | |||
| Export_ASLoOH | — | ASLoOH_c > ASLoOH_m Export_ASLoOH_k * ASLoOH_c | |||
| Export_ASLpOH | — | ASLpOH_c > ASLpOH_m Export_ASLpOH_k * ASLpOH_c | |||
| Export_ASoOH | — | ASoOH_c > ASoOH_m Export_ASoOH_k * ASoOH_c | |||
| Export_ASpOH | — | ASpOH_c > ASpOH_m Export_ASpOH_k * ASpOH_c | |||
| Import_AS | — | AS_m > AS_c Import_AS_k * AS_m | |||
| Import_ASL | — | ASL_m > ASL_c Import_ASL_k * ASL_m | |||
| Import_ASLoOH | — | ASLoOH_m > ASLoOH_c Import_ASLoOH_k * ASLoOH_m | |||
| Import_ASLpOH | — | ASLpOH_m > ASLpOH_c Import_ASLpOH_k * ASLpOH_m | |||
| Import_ASoOH | — | ASoOH_m > ASoOH_c Import_ASoOH_k * ASoOH_m | |||
| Import_ASpOH | — | ASpOH_m > ASpOH_c Import_ASpOH_k * ASpOH_m | |||
| R_ASASL_c | — | ASL_c > AS_c (k_CR_ASL_c + k_PON_ASL_c) * ASL_c | |||
| R_ASASL_m | — | ASL_m > AS_m k_CR_ASL_m * ASL_m | |||
| R_oOH_m | — | ASLoOH_m > ASoOH_m k_CR_ASL_m * ASLoOH_m | |||
| R_pOH_m | — | ASLpOH_m > ASpOH_m k_CR_ASL_m * ASLpOH_m | |||
| UGT1A3_AS | — | AS_c > ASL_c UGT1A3_AS_Vmax * AS_c / (UGT1A3_AS_Km1 + AS_c + AS_c * AS_c / UGT1A3_AS_KI1) |
| Id | Value | |
|---|---|---|
| CYP3A4_ASLoOH_Km1 | 3900.0 | |
| CYP3A4_ASLoOH_Vmax | 39.1342 | |
| CYP3A4_ASLpOH_Km1 | 1400.0 | |
| CYP3A4_ASLpOH_Vmax | 17.4446 | |
| CYP3A4_ASoOH_Km1 | 29700.0 | |
| CYP3A4_ASoOH_Vmax | 47.4985 | |
| CYP3A4_ASpOH_Km1 | 25600.0 | |
| CYP3A4_ASpOH_Vmax | 15.7336 | |
| Export_ASL_k | 0.021822 | |
| Export_ASLoOH_k | 0.0026674 | |
| Export_ASLpOH_k | 0.0011319 | |
| Export_AS_k | 0.002166 | |
| Export_ASoOH_k | 0.0015983 | |
| Export_ASpOH_k | 0.00079526 | |
| Import_ASL_k | 0.2754 | |
| Import_ASLoOH_k | 0.026122 | |
| Import_ASLpOH_k | 0.033729 | |
| Import_AS_k | 0.020335 | |
| Import_ASoOH_k | 0.00038875 | |
| Import_ASpOH_k | 0.0039614 | |
| Prot_k1 | 8.52 | |
| UGT1A3_AS_KI1 | 75000.0 | |
| UGT1A3_AS_Km1 | 12000.0 | |
| UGT1A3_AS_Vmax | 13.5862 | |
| fu_AS | 0.22 dimensionless | |
| fu_ASL | 0.22 dimensionless | |
| k_CR_ASL_c | 0.0000355 | |
| k_CR_ASL_m | 0.005 | |
| k_PON_ASL_c | 0.0043734 | |
| k_PON_OH_c | 0.0039829 |
| Id | Value | Reaction |
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| Trigger | Assignments |
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